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25 results on '"Izraelson, Mark"'

1. Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., Stepanov, Alexey V., Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey, and Chudakov, Dmitry M.

Published
2023
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3. Memory CD4+ T cells are generated in the human fetal intestine

Author

Li, Na, van Unen, Vincent, Abdelaal, Tamim, Guo, Nannan, Kasatskaya, Sofya A., Ladell, Kristin, McLaren, James E., Egorov, Evgeny S., Izraelson, Mark, Chuva de Sousa Lopes, Susana M., Höllt, Thomas, Britanova, Olga V, Eggermont, Jeroen, de Miranda, Noel F. C. C., Chudakov, Dmitriy M., Price, David A., Lelieveldt, Boudewijn P. F., and Koning, Frits

Published
2019
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4. Robust detection of SARS-CoV-2 exposure in population using T-cell repertoire profiling

Author

Vlasova, Elizaveta K, primary, Nekrasova, Alexandra I, additional, Komkov, Alexander Y, additional, Izraelson, Mark, additional, Snigir, Ekaterina A, additional, Mitrofanov, Sergey I, additional, Yudin, Vladimir S, additional, Makarov, Valentin V, additional, Kesnikov, Anton A, additional, Kirienko, Darya, additional, Pivnyuk, Anastasia, additional, Shelyakin, Pavel V, additional, Mamedov, Ilgar Z, additional, Rebrikov, Denis V, additional, Chudakov, Dmitriy M, additional, Yudin, Sergey M, additional, Skvortsova, Veronika I, additional, Britanova, Olga, additional, and Shugay, Mikhail A, additional

Published
2023
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5. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Author

Mikelov, Artem, primary, Nefedev, George, additional, Tashkeev, Aleksandr, additional, Rodriguez, Oscar L., additional, Ortmans, Diego A., additional, Skatova, Valeriia, additional, Izraelson, Mark, additional, Davydov, Alexey, additional, Poslavsky, Stanislav, additional, Rahmouni, Souad, additional, Watson, Corey T., additional, Chudakov, Dmitriy, additional, Boyd, Scott D., additional, and Bolotin, Dmitry A., additional

Published
2023
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6. Bulk TCR repertoires, Anti-TRBV9 therapy, Case report

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., A. Shagina, Irina, Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. We performed first-in-human targeted depletion of TRBV-restricted T cells in an HLA–B*27-positive patient with AS. TCR repertoires Preparation of unique molecular identifier (UMI)-labeled TCRβ cDNA libraries was performed using HUMAN TCR RNA MULTIPLEX kit (MiLaboratories) according to the manufacturer's manuals. Sequencing was performed on Illumina MiSeq and NextSeq 550, using 150+150 nt paired-end mode. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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7. Macaca mulatta, Anti-TRBV9 therapy

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., A. Shagina, Irina, Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. A single intravenous (i.v.) dose of the antibody administered to rhesus macaques (Macaca mulatta), resulted in prominent depletion of peripheral blood TRBV9+ T cells in a dose-dependent manner. Animals After quarantine, 12 Macaca mulatta males aged 5–8 years were selected for this experiment. For TCR repertoire profiling peripheral blood samples were collected before and 3, 40, 150, and 300 days after a single administration of BCD-180. We divided the animals into two groups (n = 4 for each group) that received 1 mg or 10 mg BCD-180 i.v. per animal, along with a control group that included four animals and received human intravenous IgG immunoglobulins (Microgen). Animals were kept in accordance with the guidelines for accommodation and care of laboratory animals, with species-specific provisions for nonhuman primates. The local ethics committee approved experiments for these studies. TCR repertoires Sequencing was performed on Illumina HiSeq1500. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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8. TRBV9 TCR repertoires, Anti-TRBV9 therapy, Case report

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., V. Stepanov, Alexey, Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey A., and Chudakov, Dmitry M.

Abstract

Cytotoxic humanized anti-TRBV9 monoclonal antibody. We performed first-in-human targeted depletion of TRBV-restricted T cells in an HLA–B*27-positive patient with AS. TCR repertoires Preparation of unique molecular identifier (UMI)-labeled TCRβ cDNA libraries was performed using HUMAN TCR RNA MULTIPLEX kit (MiLaboratories) according to the manufacturer's manuals. TRBV9-focused TCRβ cDNA libraries were prepared using an adapted version of the HUMAN TCR RNA MULTIPLEX kit (MiLaboratories). Sequencing was performed on Illumina MiSeq and NextSeq 550, using 150+150 nt paired-end mode. MIGEC v1.2.9 was used for UMI-based read grouping and error correction. MiXCR v3.0.13 was used for extraction of TCRβ CDR3 repertoires. VDJtools v1.2.1 was used for downstream post-analysis. The repertoires include only productive sequences with more than one read per UMI.

Published
2023
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10. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Author

Mikelov, Artem, Nefediev, George, Tashkeev, Alexander, Rodriguez, Oscar L., Aguilar Ortmans, Diego, Skatova, Valeriia, Izraelson, Mark, Davydov, Alexey N., Poslavsky, Stanislav, Rahmouni, Souad, Watson, Corey T., Chudakov, Dmitriy, Boyd, Scott D., and Bolotin, Dmitry

Abstract

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRAand TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRBloci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.

Published
2024
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11. Comparative analysis of murine T‐cell receptor repertoires

Author

Izraelson, Mark, Nakonechnaya, Tatiana O., Moltedo, Bruno, Egorov, Evgeniy S., Kasatskaya, Sofya A., Putintseva, Ekaterina V., Mamedov, Ilgar Z., Staroverov, Dmitriy B., Shemiakina, Irina I., Zakharova, Maria Y., Davydov, Alexey N., Bolotin, Dmitriy A., Shugay, Mikhail, Chudakov, Dmitriy M., Rudensky, Alexander Y., and Britanova, Olga V.

Published
2018
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12. Targeted depletion of TRBV9+T cells as immunotherapy in a patient with ankylosing spondylitis

Author

Britanova, Olga V., Lupyr, Kseniia R., Staroverov, Dmitry B., Shagina, Irina A., Aleksandrov, Alexey A., Ustyugov, Yakov Y., Somov, Dmitry V., Klimenko, Alesia, Shostak, Nadejda A., Zvyagin, Ivan V., Stepanov, Alexey V., Merzlyak, Ekaterina M., Davydov, Alexey N., Izraelson, Mark, Egorov, Evgeniy S., Bogdanova, Ekaterina A., Vladimirova, Anna K., Iakovlev, Pavel A., Fedorenko, Denis A., Ivanov, Roman A., Skvortsova, Veronika I., Lukyanov, Sergey, and Chudakov, Dmitry M.

Abstract

Autoimmunity is intrinsically driven by memory T and B cell clones inappropriately targeted at self-antigens. Selective depletion or suppression of self-reactive T cells remains a holy grail of autoimmune therapy, but disease-associated T cell receptors (TCRs) and cognate antigenic epitopes remained elusive. A TRBV9-containing CD8+TCR motif was recently associated with the pathogenesis of ankylosing spondylitis, psoriatic arthritis and acute anterior uveitis, and cognate HLA-B*27-presented epitopes were identified. Following successful testing in nonhuman primate models, here we report human TRBV9+T cell elimination in ankylosing spondylitis. The patient achieved remission within 3 months and ceased anti-TNF therapy after 5 years of continuous use. Complete remission has now persisted for 4 years, with three doses of anti-TRBV9 administered per year. We also observed a profound improvement in spinal mobility metrics and the Bath Ankylosing Spondylitis Metrology Index (BASMI). This represents a possibly curative therapy of an autoimmune disease via selective depletion of a TRBV-defined group of T cells. The anti-TRBV9 therapy could potentially be applicable to other HLA-B*27-associated spondyloarthropathies. Such targeted elimination of the underlying cause of the disease without systemic immunosuppression could offer a new generation of safe and efficient therapies for autoimmunity.

Published
2023
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13. Functionally specialized human CD4+ T-cell subsets express physicochemically distinct TCRs

Author

Kasatskaya, Sofya A, primary, Ladell, Kristin, additional, Egorov, Evgeniy S, additional, Miners, Kelly L, additional, Davydov, Alexey N, additional, Metsger, Maria, additional, Staroverov, Dmitry B, additional, Matveyshina, Elena K, additional, Shagina, Irina A, additional, Mamedov, Ilgar Z, additional, Izraelson, Mark, additional, Shelyakin, Pavel V, additional, Britanova, Olga V, additional, Price, David A, additional, and Chudakov, Dmitriy M, additional

Published
2020
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14. Author response: Functionally specialized human CD4+ T-cell subsets express physicochemically distinct TCRs

Author

Kasatskaya, Sofya A, primary, Ladell, Kristin, additional, Egorov, Evgeniy S, additional, Miners, Kelly L, additional, Davydov, Alexey N, additional, Metsger, Maria, additional, Staroverov, Dmitry B, additional, Matveyshina, Elena K, additional, Shagina, Irina A, additional, Mamedov, Ilgar Z, additional, Izraelson, Mark, additional, Shelyakin, Pavel V, additional, Britanova, Olga V, additional, Price, David A, additional, and Chudakov, Dmitriy M, additional

Published
2020
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15. Measuring Intratumoral Heterogeneity of Immune Repertoires

Author

Yuzhakova, Diana Vladimirovna, primary, Volchkova, Lilia N., additional, Pogorelyy, Mikhail Valerievich, additional, Serebrovskaya, Ekaterina O., additional, Shagina, Irina A., additional, Bryushkova, Ekaterina A., additional, Nakonechnaya, Tatiana O., additional, Izosimova, Anna V., additional, Zavyalova, Daria S., additional, Karabut, Maria M., additional, Izraelson, Mark, additional, Samoylenko, Igor V., additional, Zagainov, Vladimir E., additional, Chudakov, Dmitriy M., additional, Zagaynova, Elena V., additional, and Sharonov, George Vladimirovich, additional

Published
2020
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17. The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging

Author

Egorov, Evgeny S., primary, Kasatskaya, Sofya A., additional, Zubov, Vasiliy N., additional, Izraelson, Mark, additional, Nakonechnaya, Tatiana O., additional, Staroverov, Dmitriy B., additional, Angius, Andrea, additional, Cucca, Francesco, additional, Mamedov, Ilgar Z., additional, Rosati, Elisa, additional, Franke, Andre, additional, Shugay, Mikhail, additional, Pogorelyy, Mikhail V., additional, Chudakov, Dmitriy M., additional, and Britanova, Olga V., additional

Published
2018
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18. Comparative analysis of murine T-cell receptor repertoires

Author

Izraelson, Mark, primary, Nakonechnaya, Tatiana O., additional, Moltedo, Bruno, additional, Egorov, Evgeniy S., additional, Kasatskaya, Sofya A., additional, Putintseva, Ekaterina V., additional, Mamedov, Ilgar Z., additional, Staroverov, Dmitriy B., additional, Shemiakina, Irina I., additional, Zakharova, Maria Y., additional, Davydov, Alexey N., additional, Bolotin, Dmitriy A., additional, Shugay, Mikhail, additional, Chudakov, Dmitriy M., additional, Rudensky, Alexander Y., additional, and Britanova, Olga V., additional

Published
2017
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19. Wnt/β-Catenin Signaling Induces Integrin α4β1 in T Cells and Promotes a Progressive Neuroinflammatory Disease in Mice

Author

Sorcini, Daniele, primary, Bruscoli, Stefano, additional, Frammartino, Tiziana, additional, Cimino, Monica, additional, Mazzon, Emanuela, additional, Galuppo, Maria, additional, Bramanti, Placido, additional, Al-Banchaabouchi, Mumna, additional, Farley, Dominika, additional, Ermakova, Olga, additional, Britanova, Olga, additional, Izraelson, Mark, additional, Chudakov, Dmitry, additional, Biagioli, Michele, additional, Sportoletti, Paolo, additional, Flamini, Sara, additional, Raspa, Marcello, additional, Scavizzi, Ferdinando, additional, Nerlov, Claus, additional, Migliorati, Graziella, additional, Riccardi, Carlo, additional, and Bereshchenko, Oxana, additional

Published
2017
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20. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

Author

Britanova, Olga V., primary, Shugay, Mikhail, additional, Merzlyak, Ekaterina M., additional, Staroverov, Dmitriy B., additional, Putintseva, Ekaterina V., additional, Turchaninova, Maria A., additional, Mamedov, Ilgar Z., additional, Pogorelyy, Mikhail V., additional, Bolotin, Dmitriy A., additional, Izraelson, Mark, additional, Davydov, Alexey N., additional, Egorov, Evgeny S., additional, Kasatskaya, Sofya A., additional, Rebrikov, Denis V., additional, Lukyanov, Sergey, additional, and Chudakov, Dmitriy M., additional

Published
2016
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22. Memory CD4+T cells are generated in the human fetal intestine

Author

Li, Na, van Unen, Vincent, Abdelaal, Tamim, Guo, Nannan, Kasatskaya, Sofya A., Ladell, Kristin, McLaren, James E., Egorov, Evgeny S., Izraelson, Mark, Chuva de Sousa Lopes, Susana M., Höllt, Thomas, Britanova, Olga V, Eggermont, Jeroen, de Miranda, Noel F. C. C., Chudakov, Dmitriy M., Price, David A., Lelieveldt, Boudewijn P. F., and Koning, Frits

Abstract

The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+T cells reside in the fetal intestine. Here we combined functional assays with mass cytometry, single-cell RNA sequencing and high-throughput T cell antigen receptor (TCR) sequencing to characterize the CD4+T cell compartment in the human fetal intestine. We identified 22 CD4+T cell clusters, including naive-like, regulatory-like and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like CD4+T cells had high expression of Ki-67, indicative of cell division, and CD5, a surrogate marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR repertoire analysis indicated clonal expansions, distinct repertoire characteristics and interconnections between subpopulations of memory-like CD4+T cells. Imaging mass cytometry indicated that memory-like CD4+T cells colocalized with antigen-presenting cells. Collectively, these results provide evidence for the generation of memory-like CD4+T cells in the human fetal intestine that is consistent with exposure to foreign antigens.

Published
2019
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23. DNA repair in Mycoplasma gallisepticum

Author

Gorbachev, Alexey Y, primary, Fisunov, Gleb Y, additional, Izraelson, Mark, additional, Evsyutina, Darya V, additional, Mazin, Pavel V, additional, Alexeev, Dmitry G, additional, Pobeguts, Olga V, additional, Gorshkova, Tatyana N, additional, Kovalchuk, Sergey I, additional, Kamashev, Dmitry E, additional, and Govorun, Vadim M, additional

Published
2013
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24. Wnt/β-Catenin Signaling Induces Integrin a4b1 in T Cells and Promotes a Progressive Neuroinflammatory Disease in Mice.

Author

Sorcini, Daniele, Bruscoli, Stefano, Frammartino, Tiziana, Cimino, Monica, Mazzon, Emanuela, Galuppo, Maria, Bramanti, Placido, Al-Banchaabouchi, Mumna, Farley, Dominika, Ermakova, Olga, Britanova, Olga, Izraelson, Mark, Chudakov, Dmitry, Biagioli, Michele, Sportoletti, Paolo, Flamini, Sara, Raspa, Marcello, Scavizzi, Ferdinando, Nerlov, Claus, and Migliorati, Graziella

Subjects
*INTEGRINS, *T cells, *LABORATORY mice, *GENE expression, *INFLAMMATION
Abstract

The mechanisms leading to autoimmune and inflammatory diseases in the CNS have not been elucidated. The environmental triggers of the aberrant presence of CD4+ T cells in the CNS are not known. In this article, we report that abnormal β-catenin expression in T cells drives a fatal neuroinflammatory disease in mice that is characterized by CNS infiltration of T cells, glial activation, and progressive loss of motor function. We show that enhanced β-catenin expression in T cells leads to aberrant and Th1-biased T cell activation, enhanced expression of integrin α4β1, and infiltration of activated T cells into the spinal cord, without affecting regulatory T cell function. Importantly, expression of β-catenin in mature naive T cells was sufficient to drive integrin α4β1 expression and CNS migration, whereas pharmacologic inhibition of integrin α4β1 reduced the abnormal T cell presence in the CNS of β-catenin--expressing mice. Together, these results implicate deregulation of the Wnt/β-catenin pathway in CNS inflammation and suggest novel therapeutic strategies for neuroinflammatory disorders. [ABSTRACT FROM AUTHOR]

Published
2017
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25. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.

Author

Mikelov A, Nefediev G, Tashkeev A, Rodriguez OL, Ortmans DA, Skatova V, Izraelson M, Davydov A, Poslavsky S, Rahmouni S, Watson CT, Chudakov D, Boyd SD, and Bolotin D

Abstract

Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), has been shown to be of critical importance for immune responses to pathogens and vaccines. In recent years, B cell and T cell receptor repertoire sequencing (Rep-Seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci in different populations. Here we present a novel algorithm for extra-sensitive and specific variable (V) and joining (J) gene allele inference and genotyping allowing reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput genotyping and novel allele discovery from a wide variety of existing datasets. The developed algorithm is a part of the MiXCR software ( https://mixcr.com ) and can be incorporated into any pipeline utilizing upstream processing with MiXCR. We demonstrate the accuracy of this approach using Rep-Seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) Rep-Seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA; TRB) Rep-Seq dataset, representing 134 individuals. This allowed us to assess the genetic diversity of genes within the IGH, TRA and TRB loci in different populations and demonstrate the connection between antibody repertoire gene usage and the number of allelic variants present in the population. Finally we established a database of allelic variants of V and J genes inferred from Rep-Seq data and their population frequencies with free public access at https://vdj.online .

Published
2023
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